One function of the hyphen is to prevent misreading. For example, the shortened form of the noun meaning “an enterprise or organization owned by and operated for the benefit of those using its services” is co-op, to distinguish it from the English word coop: “a cage or small enclosure for poultry or other small animals.”
Co-op is a shortening of the word spelled co-operative in the OED, but cooperative in Merriam-Webster.
The Oxford English Dictionary and Merriam-Webster agree some of the time, but generally speaking, the OED is more likely than M-W to hyphenate. Here are some examples:
According to The Chicago Manual of Style, compounds formed with prefixes are closed, whether they are nouns, verbs, adjectives, or adverbs. For example:
Note: The Word spell-checker suggests Neo-Platonism, but the OED and Merriam-Webster Unabridged give Neoplatonism.
A hyphen is used when the prefix precedes a capitalized word or a numeral:
A hyphen is used to avoid misreading when the prefix ends with the same letter that begins the word element that follows:
anti-intellectual (not antiintellectual)
pre-emptory (not preemptory)
When it comes to hyphens, authorities do not always agree. The best practice is to adopt a style guide or dictionary and follow its recommendations.